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- PDB-7bjg: Crystal structure of atypical Tm1 (Tm1-I/C), residues 262-363 -

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Basic information

Entry
Database: PDB / ID: 7bjg
TitleCrystal structure of atypical Tm1 (Tm1-I/C), residues 262-363
ComponentsSD21996p
KeywordsTRANSPORT PROTEIN / coiled-coil / Drosophila oocyte / binds Khc / RNA transport
Function / homologyTropomyosin / Tropomyosin / SD21996p
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDimitrova-Paternoga, L. / Jagtap, P.K.A. / Ephrussi, A. / Hennig, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP 1935 Germany
CitationJournal: Genes Dev. / Year: 2021
Title: Molecular basis of mRNA transport by a kinesin-1-atypical tropomyosin complex.
Authors: Dimitrova-Paternoga, L. / Jagtap, P.K.A. / Cyrklaff, A. / Lapouge, K. / Sehr, P. / Perez, K. / Heber, S. / Low, C. / Hennig, J. / Ephrussi, A.
History
DepositionJan 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SD21996p


Theoretical massNumber of molelcules
Total (without water)11,9221
Polymers11,9221
Non-polymers00
Water34219
1
A: SD21996p

A: SD21996p


Theoretical massNumber of molelcules
Total (without water)23,8452
Polymers23,8452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+11
Buried area2990 Å2
ΔGint-28 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.030, 107.030, 52.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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Components

#1: Protein SD21996p / Tropomyosin 1 / isoform H


Mass: 11922.319 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Tm1, 10, 1305, 2299, BcDNA:GH09289, BcDNA:LD37158, BcDNA:SD21996, chr3R:11122272..11122408, cTM, cTm, cTmII, Dm Tm1, Dm TmH33, Dm TmH34, Dmel\CG4898, DmTm1, l(3)02299, l(3)S130510, l(3)s2958, ...Gene: Tm1, 10, 1305, 2299, BcDNA:GH09289, BcDNA:LD37158, BcDNA:SD21996, chr3R:11122272..11122408, cTM, cTm, cTmII, Dm Tm1, Dm TmH33, Dm TmH34, Dmel\CG4898, DmTm1, l(3)02299, l(3)S130510, l(3)s2958, mTmII, PmI, region 3, TM, Tm, TM1, tm1, TmH, TmH-33, TmH-34, TmH33, TmH34, TMII, TmII, tmII, Tmr33, Tmr34, TnH, TnH-33, TnH-34, tropomyosin, CG4898, Dmel_CG4898
Production host: Escherichia coli (E. coli) / References: UniProt: Q8IG84
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris-HCl pH8, 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.45→53.52 Å / Num. obs: 6906 / % possible obs: 99.1 % / Redundancy: 18.711 % / Biso Wilson estimate: 69.318 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.094 / Χ2: 0.98 / Net I/σ(I): 17.55 / Num. measured all: 129216
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.45-2.5118.1241.0672.2189355094930.9421.09796.9
2.51-2.5819.9810.8083.2393914754700.9580.82998.9
2.58-2.6519.3050.6134.2391704834750.9820.6398.3
2.65-2.7419.3120.5524.7985554514430.9840.56798.2
2.74-2.8318.1420.3527.1880554524440.9920.36398.2
2.83-2.9219.0420.2410.9781884354300.9940.24798.9
2.92-3.0419.9090.21612.6581034124070.9950.22298.8
3.04-3.1619.2920.17215.3778714114080.9960.17799.3
3.16-3.319.1920.15517.9774853913900.9950.15999.7
3.3-3.4618.0770.12220.3967973763760.9970.126100
3.46-3.6518.9220.10525.0167553573570.9980.108100
3.65-3.8719.3640.09128.8766423433430.9980.093100
3.87-4.1419.0190.08131.4261623243240.9970.084100
4.14-4.4717.9270.07232.7354323033030.9980.074100
4.47-4.8918.1640.07333.8150862812800.9990.07699.6
4.89-5.4718.8860.07332.847972552540.9990.07599.6
5.47-6.3217.9580.08629.8242382362360.9980.089100
6.32-7.7416.6040.07233.5333542032020.9980.07599.5
7.74-10.9416.6610.06537.6327491661650.9990.06799.4
10.94-53.5213.6890.06335.0314511091060.9990.06697.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
AMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly A helix

Resolution: 2.45→53.52 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 39.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2941 344 5 %
Rwork0.2522 6542 -
obs0.2543 6886 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.53 Å2 / Biso mean: 74.5063 Å2 / Biso min: 38.58 Å2
Refinement stepCycle: final / Resolution: 2.45→53.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms778 0 0 19 797
Biso mean---74.78 -
Num. residues----98
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-3.080.39681650.3293148331398
3.08-53.520.27341790.236833943573100

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